A frequent problem in forecasting fog or icy roads in a numerical weather prediction system is attributed to the misinterpretation of the boundary layer structure in the assimilation procedure. Case studies showed that much of the misinterpretation of temperature inversions and stratocumulus layers in the assimilation is due to inappropriate background error covariances. This paper looks at the application of adaptive mesh methods in the Met Office variational assimilation system to modify the background error correlations in the boundary layer when temperature inversions or stratocumulus layers are present in the background state.